scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of single-cell eQTLs

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Documentation for package ‘scQTLtools’ version 1.1.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

adjust_pvalues	Adjust p-values and filter SNP–gene pairs based on the adjusted p-values.
buildZINB	Build a ZINB model.
callQTL	Identify single-cell eQTLs.
checkSNPList	Validate SNP IDs in the input genotype matrix.
CPM_normalize	Normalize gene expression using CPM.
createGeneLoc	Create a gene location data frame.
createQTLObject	Create an eQTLObject for storing sc-eQTL analysis data.
createSNPsLoc	Create SNP location dataframe.
DataSet	The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.
DESeq_normalize	Normalize the gene expression matrix with DESeq2.
draw_boxplot	Generate a boxplot of gene expression by SNP genotype.
draw_histplot	Generate a histogram of gene expression by SNP genotype.
draw_QTLplot	Create a combined violin-box-scatter plot.
draw_violinplot	Generate a violin plot of gene expression by SNP genotype.
eQTLObject-class	Class 'eQTLObject'
EQTL_obj	The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.
filterGeneSNP	Filter gene expression and genotype matrices by cell percentage thresholds.
filter_by_abs_b	Filter a data frame of SNP–gene pairs by absolute beta.
GeneData	The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.
get_cell_groups	Retrieve Cells by SNP Value
get_counts	Extract Counts from an Expression Matrix
get_filter_data	Access filtered data stored in an eQTLObject.
get_filter_data-method	Access filtered data stored in an eQTLObject.
get_model_info	Access model specification from an eQTLObject
get_model_info-method	Access model specification from an eQTLObject
get_raw_data	Access raw data stored in an eQTLObject.
get_raw_data-method	Access raw data stored in an eQTLObject.
get_result_info	Access eQTLs results from an eQTLObject.
get_result_info-method	Access eQTLs results from an eQTLObject.
initialize_progress_bar	Progress Bar for Model Analysis.
limma_normalize	Normalize the gene expression matrix with limma
linearModel	Fit Linear Model for eQTL Mapping
load_biclassify_info	Access biclassification information from an eQTLObject.
load_biclassify_info-method	Access biclassification information from an eQTLObject.
load_group_info	Access cell grouping information from an eQTLObject
load_group_info-method	Access cell grouping information from an eQTLObject
load_species_info	Access species information from an eQTLObject.
load_species_info-method	Access species information from an eQTLObject.
log_normalize	Normalize the gene expression matrix with logNormalize method.
normalizeGene	Normalize gene expression data.
plots_theme_opts	Customized ggplot2 Theme for Plots
poissonModel	Poisson model fitting the gene expression matrix and genotype matrix.
process_matrix	Process a matrix to extract a row and convert it to a data frame.
remove_outliers	Remove outliers from gene expression data and update cell groups.
set_filter_data	Set filtered data in an eQTLObject.
set_filter_data-method	Set filtered data in an eQTLObject.
set_model_info	Set model specification in an eQTLObject
set_model_info-method	Set model specification in an eQTLObject
set_raw_data	Set raw data in an eQTLObject.
set_raw_data-method	Set raw data in an eQTLObject.
set_result_info	Set eQTL results in an eQTLObject.
set_result_info-method	Set eQTL results in an eQTLObject.
Seurat_obj	The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.
SNPData	The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.
SNPData2	The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.
TPM_normalize	Normalize the gene expression matrix with TPM
visualizeQTL	Visualize eQTL results by SNP–gene pair across groups
zinbModel	Zinb model fitting the gene expression matrix.